Agent Skill · cast

freeform-summary-to-galaxy-data-flow

Translate a free-form source summary into a Galaxy data-flow design brief.

Install with Claude Code

/plugin marketplace add galaxyproject/foundry
/plugin install foundry-skills@galaxy-workflow-foundry

Then invoke as:

/foundry-skills:freeform-summary-to-galaxy-data-flow

Install with Codex

codex plugin marketplace add galaxyproject/foundry
codex plugin add foundry-skills@galaxy-workflow-foundry

Then select with /skills or invoke explicitly as:

$freeform-summary-to-galaxy-data-flow

Install with Antigravity

git clone https://github.com/galaxyproject/foundry
agy plugin install foundry/casts/claude

Then select with /skills or invoke explicitly as:

/freeform-summary-to-galaxy-data-flow

Skill Bundle

/ packaged cast

attached files: 7
upfront: 2
on demand: 5
cast rev: n/a
validated: 0

Produces: 2 artifacts.

Consumes: 3 artifacts.

Artifact Contract

/ skill handoff

Produces

freeform-galaxy-data-flow

Reviewable Markdown brief: abstract operations, collection map/reduce choices, shape-changing placeholder steps, unresolved Galaxy tool needs, confidence, open questions.

markdownfreeform-galaxy-data-flow.md

Raw artifact contract

{
  "id": "freeform-galaxy-data-flow",
  "kind": "markdown",
  "default_filename": "freeform-galaxy-data-flow.md",
  "description": "Reviewable Markdown brief: abstract operations, collection map/reduce choices, shape-changing placeholder steps, unresolved Galaxy tool needs, confidence, open questions."
}

open-requirements-ledger

Carried obligations ledger re-emitted by this step: entries it appended or closed updated, every other entry passed through with its provenance intact.

yamlopen-requirements.ledger.yml

Raw artifact contract

{
  "id": "open-requirements-ledger",
  "kind": "yaml",
  "default_filename": "open-requirements.ledger.yml",
  "description": "Carried obligations ledger re-emitted by this step: entries it appended or closed updated, every other entry passed through with its provenance intact."
}

Consumes

freeform-summary

Free-form source summary emitted by [[summarize-paper]] or [[interview-to-freeform-summary]]; consumed alongside the Galaxy interface brief.

Raw artifact contract

{
  "id": "freeform-summary",
  "description": "Free-form source summary emitted by [[summarize-paper]] or [[interview-to-freeform-summary]]; consumed alongside the Galaxy interface brief.",
  "producers": [
    "interview-to-freeform-summary",
    "summarize-paper"
  ]
}

freeform-galaxy-interface

Preceding Galaxy interface brief from [[freeform-summary-to-galaxy-interface]] that pins inputs, outputs, and labels.

Raw artifact contract

{
  "id": "freeform-galaxy-interface",
  "description": "Preceding Galaxy interface brief from [[freeform-summary-to-galaxy-interface]] that pins inputs, outputs, and labels.",
  "producers": [
    "freeform-summary-to-galaxy-interface"
  ]
}

open-requirements-ledger

Carried obligations ledger [[open-requirements-ledger]]: the run's open, resolved, and surrendered entries with their provenance. Absent on the first Mold of a run; start an empty one.

Raw artifact contract

{
  "id": "open-requirements-ledger",
  "description": "Carried obligations ledger [[open-requirements-ledger]]: the run's open, resolved, and surrendered entries with their provenance. Absent on the first Mold of a run; start an empty one.",
  "producers": [
    "advance-galaxy-draft-step",
    "apply-galaxy-workflow-changeset",
    "compare-against-iwc-exemplar",
    "cwl-summary-to-galaxy-data-flow",
    "cwl-summary-to-galaxy-interface",
    "cwl-summary-to-galaxy-template",
    "freeform-summary-to-galaxy-data-flow",
    "freeform-summary-to-galaxy-interface",
    "freeform-summary-to-galaxy-template",
    "implement-galaxy-tool-step",
    "interview-to-galaxy-workflow-changeset",
    "mature-galaxy-workflow-for-iwc",
    "nextflow-summary-to-galaxy-data-flow",
    "nextflow-summary-to-galaxy-interface",
    "nextflow-summary-to-galaxy-reference-data",
    "nextflow-summary-to-galaxy-template",
    "repair-galaxy-draft-topology"
  ]
}

Attached Files

/ runtime references

Load upfront

research

galaxy-data-flow-draft-contract

packaged

Keep the data-flow brief separate from gxformat2 templating and concrete step implementation.

upfront runtime verbatim hypothesis deterministic 7.3 KB

bundle: references/notes/galaxy-data-flow-draft-contract.md
source: content/research/galaxy-data-flow-draft-contract/index.md

Preview md

---
type: research
title: "Galaxy data-flow draft contract"
tags:
  - target/galaxy
status: draft
created: 2026-05-02
revised: 2026-05-03
revision: 2
related_notes:
  - "[[nextflow-to-galaxy-channel-shape-mapping]]"
  - "[[nextflow-operators-to-galaxy-collection-recipes]]"
  - "[[galaxy-workflow-draft]]"
related_molds:
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[cwl-summary-to-galaxy-data-flow]]"
  - "[[freeform-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[freeform-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
  - "[[advance-galaxy-draft-step]]"
sources:
  - "https://github.com/galaxyproject/foundry/issues/54"
summary: "Defines the proposed boundary between Galaxy data-flow drafts, gxformat2 templates, and concrete step implementation."
---

# Galaxy Data-Flow Draft Contract

This is an architectural contract, not a schema. Evidence is strongest for Mold and Pipeline boundaries. Proposed fields are speculative until exercised by two or three worked translations.

## Boundary

The data-flow draft owns a target-shaped abstract DAG for Galaxy. It should not be valid `gxformat2` and should not resolve exact Tool Shed tools.

Data-flow draft owns:

- Galaxy-facing workflow inputs and outputs.
- Abstract nodes, edges, branches, collection mapping, collection reduction, and placeholder transformations.
- Input/output shape decisions such as `File`, `list`, `paired`, `list:paired`, or `list:list`.
- Conceptual Galaxy idioms: map-over, reduction, Apply Rules, collection cleanup, identifier synchronization, tabular bridge, fan-in / combine (concatenate, merge, or union N sources into one — a distinct node, not a side-effect of a reshape).
- Abstract unresolved tool nee
...

research

open-requirements-ledger

packaged

Inherit open entries rather than re-deriving them, close the ones this brief's wiring and collection decisions settle, and append data-flow obligations the narrative leaves open — a described transformation with no named tool, an implied intermediate the source never states, an ordering the prose doesn't fix.

upfront runtime verbatim hypothesis deterministic 15.5 KB

bundle: references/notes/open-requirements-ledger.md
source: content/research/open-requirements-ledger/index.md

Preview md

---
type: research
title: "Open-requirements ledger"
tags:
  - target/galaxy
status: draft
created: 2026-06-16
revised: 2026-08-29
revision: 3
related_notes:
  - "[[galaxy-workflow-draft-format]]"
related_molds:
  - "[[advance-galaxy-draft-step]]"
  - "[[repair-galaxy-draft-topology]]"
  - "[[implement-galaxy-tool-step]]"
summary: "Carried unresolved-requirements artifact the source→Galaxy pipeline discharges or explicitly surrenders, autonomously."
---

# Open-requirements ledger

The `open-requirements-ledger` is a single artifact threaded through the source→Galaxy pipeline that records **obligations the pipeline has taken on but not yet met** — a declared output with no producer, a parameter whose value the source never pinned, a tool with no corpus exemplar — and **source work it decided not to carry**. Each Mold that surfaces one **appends** it; each Mold whose decision closes one **marks it resolved**; the terminal path **surrenders** whatever remains open, explicitly, into the final artifact.

## Framing: obligations the pipeline discharges, not questions a human answers

This is deliberately *not* an "open questions for the user" list. The pipeline is autonomous — no human-in-the-loop gate is assumed. The ledger's consumers are **Molds and the loop's convergence gate**, with human readout a secondary affordance. An entry is closed by a downstream Mold doing work (wiring a producer, picking a wrapper, settling a value), or — when nothing can close it — surrendered: written into the final draft as a known, labelled gap rather than silently dropped or fabricated around.

The distinction matters because a "questions for a human" framing leaks an operator's personal interaction style into a tool meant to run inside anyone's harness. The ledger must behave identically
...

Load on demand

pattern

galaxy-collection-patterns

packaged

Ground collection-shape choices in curated, corpus-observed operation and recipe patterns.

Trigger: When selecting collection cleanup, reshape, identifier, or collection-tabular bridge patterns.

on-demand runtime verbatim corpus-observed deterministic 6.1 KB

bundle: references/patterns/galaxy-collection-patterns.md
source: content/patterns/galaxy-collection-patterns.md

Preview md

---
type: pattern
pattern_kind: moc
evidence: corpus-observed
title: "Galaxy: collection patterns"
aliases:
  - "Galaxy collection pattern MOC"
  - "collection transformation patterns"
  - "IWC collection pattern map"
tags:
  - target/galaxy
  - topic/galaxy-transform
  - topic/collection-transform
status: draft
created: 2026-05-02
revised: 2026-09-22
revision: 2
summary: "Choose a Galaxy collection operation or map-over recipe from the current and required data shapes."
related_notes:
  - "[[iwc-transformations-survey]]"
  - "[[iwc-conditionals-survey]]"
related_patterns:
  - "[[manifest-to-mapped-collection-lifecycle]]"
  - "[[cleanup-sync-and-publish-nonempty-results]]"
  - "[[reshape-relabel-remap-by-collection-axis]]"
  - "[[fan-in-bundle-consume-and-flatten]]"
  - "[[collection-cleanup-after-mapover-failure]]"
  - "[[collection-unbox-singleton]]"
  - "[[sync-collections-by-identifier]]"
  - "[[harmonize-by-sortlist-from-identifiers]]"
  - "[[regex-relabel-via-tabular]]"
  - "[[relabel-via-rules-and-find-replace]]"
  - "[[collection-flatten-after-fanout]]"
  - "[[collection-build-named-bundle]]"
  - "[[collection-swap-nesting-with-apply-rules]]"
  - "[[collection-split-identifier-via-rules]]"
  - "[[collection-build-list-paired-with-apply-rules]]"
  - "[[tabular-to-collection-by-row]]"
  - "[[tabular-concatenate-collection-to-table]]"
  - "[[tabular-pivot-collection-to-wide]]"
related_molds:
  - "[[implement-galaxy-tool-step]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[cwl-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[freeform-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
---

# Galaxy: collection patterns

Choose by the collection you have and the shap
...

pattern

galaxy-conditionals-patterns

packaged

Ground conditional-branch and optional-step choices in curated, corpus-observed Galaxy when/pick_value patterns.

Trigger: When data-flow translation needs optional steps, gating on non-empty results, routing between alternative outputs, or transform-or-pass-through branches.

on-demand runtime verbatim corpus-observed deterministic 3.5 KB

bundle: references/patterns/galaxy-conditionals-patterns.md
source: content/patterns/galaxy-conditionals-patterns.md

Preview md

---
type: pattern
pattern_kind: moc
evidence: corpus-observed
title: "Galaxy: conditionals patterns"
aliases:
  - "Galaxy conditional pattern MOC"
  - "Galaxy when patterns"
  - "conditional workflow patterns"
tags:
  - target/galaxy
  - topic/galaxy-transform
status: draft
created: 2026-05-02
revised: 2026-09-23
revision: 2
summary: "Choose a Galaxy when gate, routed output, fallback, or collection cleanup by what must change downstream."
related_notes:
  - "[[iwc-conditionals-survey]]"
related_patterns:
  - "[[conditional-run-optional-step]]"
  - "[[conditional-route-between-alternative-outputs]]"
  - "[[conditional-gate-on-nonempty-result]]"
  - "[[conditional-transform-or-pass-through]]"
  - "[[collection-cleanup-after-mapover-failure]]"
related_molds:
  - "[[implement-galaxy-tool-step]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[cwl-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[freeform-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
---

# Galaxy: conditionals patterns

Choose by what should happen when the condition is false: skip a step, select one value for a continuing path, or remove unusable collection members. The linked pages give the construction details. The [[iwc-conditionals-survey]] records the IWC evidence behind them.

Galaxy steps in the observed patterns receive a boolean through an input named `when` and declare `when: $(inputs.when)`. If later steps require an output from a skipped branch, give them an explicit merge or fallback. A `when` gate alone does not provide that value.

## Skip work without replacing its output

- **User choice or another available boolean:** [[conditional-run-optional-step]] gates an optional step or branch w
...

pattern

galaxy-interval-patterns

packaged

Ground genomic-interval operation choices in curated, corpus-observed Galaxy interval recipes.

Trigger: When the workflow operates on genomic intervals (BED/GFF/VCF coordinate features) and data-flow translation needs overlap, merge, coverage, windowing, masking, or set-algebra steps.

on-demand runtime verbatim corpus-observed deterministic 5.5 KB

bundle: references/patterns/galaxy-interval-patterns.md
source: content/patterns/galaxy-interval-patterns.md

Preview md

---
type: pattern
pattern_kind: moc
evidence: corpus-observed
title: "Galaxy: genomic interval patterns"
aliases:
  - "Galaxy interval pattern MOC"
  - "genomic interval transformation patterns"
  - "IWC interval pattern map"
tags:
  - target/galaxy
  - topic/galaxy-transform
  - topic/interval-transform
status: draft
created: 2026-06-10
revised: 2026-08-03
revision: 2
summary: "Use this MOC to choose corpus-grounded Galaxy genomic interval operations and recipes on coordinate features."
related_notes:
  - "[[iwc-interval-operations-survey]]"
related_patterns:
  - "[[interval-overlap-filter]]"
  - "[[interval-coverage]]"
  - "[[interval-merge-overlapping]]"
  - "[[interval-window-flank]]"
  - "[[interval-consensus-by-multi-intersect]]"
  - "[[interval-mask-by-set-algebra]]"
  - "[[interval-windowed-coverage]]"
  - "[[tabular-synthesize-bed-from-3col]]"
related_molds:
  - "[[implement-galaxy-tool-step]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[cwl-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[freeform-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
---

# Galaxy: genomic interval patterns

The runtime-facing map for Galaxy **coordinate-feature** choices — operations that understand `chrom/start/end/strand`, as opposed to opaque-column [[galaxy-tabular-patterns]] or container-shaped [[galaxy-collection-patterns]]. Use it before loading raw survey notes; [[iwc-interval-operations-survey]] is the evidence backing, these pages are the actionable references.

This is the smallest of the three data-shape MOCs by design. Interval algebra is a real but moderate cluster in IWC — concentrated in epigenetics peak-consensus and SARS-CoV-2 masking — and its highest-value 
...

pattern

galaxy-tabular-patterns

packaged

Ground tabular bridge and table-operation choices in curated, corpus-observed operation patterns.

Trigger: When data-flow translation needs filtering, joining, aggregation, pivoting, or tabular-collection bridges.

on-demand runtime verbatim corpus-observed deterministic 4.8 KB

bundle: references/patterns/galaxy-tabular-patterns.md
source: content/patterns/galaxy-tabular-patterns.md

Preview md

---
type: pattern
pattern_kind: moc
evidence: corpus-observed
title: "Galaxy: tabular patterns"
aliases:
  - "Galaxy tabular pattern MOC"
  - "tabular transformation patterns"
  - "IWC tabular pattern map"
tags:
  - target/galaxy
  - topic/galaxy-transform
  - topic/tabular-transform
status: draft
created: 2026-05-02
revised: 2026-09-22
revision: 2
summary: "Use this MOC to choose corpus-grounded Galaxy tabular transformation patterns."
related_notes:
  - "[[iwc-tabular-operations-survey]]"
related_patterns:
  - "[[tabular-filter-by-column-value]]"
  - "[[tabular-filter-by-regex]]"
  - "[[tabular-cut-and-reorder-columns]]"
  - "[[tabular-compute-new-column]]"
  - "[[tabular-join-on-key]]"
  - "[[tabular-group-and-aggregate-with-datamash]]"
  - "[[tabular-sql-query]]"
  - "[[tabular-prepend-header]]"
  - "[[tabular-synthesize-bed-from-3col]]"
  - "[[tabular-split-taxonomy-string]]"
  - "[[tabular-relabel-by-row-counter]]"
  - "[[tabular-to-collection-by-row]]"
  - "[[tabular-concatenate-collection-to-table]]"
  - "[[tabular-pivot-collection-to-wide]]"
related_molds:
  - "[[implement-galaxy-tool-step]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[cwl-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[freeform-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
---

# Galaxy: tabular patterns

Choose by the shape of the input and the result you need. These patterns treat table columns as values, even when a column contains coordinates or sequence text. For coordinate-aware operations use [[galaxy-interval-patterns]], and for FASTA records use [[galaxy-sequence-patterns]]. Open the linked operation page for tool parameters and examples. [[iwc-tabular-operations-survey]] reco
...

research

galaxy-sample-sheet-collections

packaged

Preserve per-row metadata on the data-flow side: keep sample_sheet column_definitions wired through identifier-keyed steps instead of dropping into parallel parameter inputs, and re-attach metadata after map-over steps that lose it.

Trigger: When the interface brief carries a sample_sheet[:paired|:paired_or_unpaired|:record] input, or the free-form summary describes per-sample/per-record metadata that must survive map-over steps.

on-demand runtime verbatim corpus-observed deterministic 8.4 KB

bundle: references/notes/galaxy-sample-sheet-collections.md
source: content/research/galaxy-sample-sheet-collections/index.md

Preview md

---
type: research
title: "Galaxy sample_sheet collection types"
tags:
  - target/galaxy
status: draft
created: 2026-05-05
revised: 2026-05-06
revision: 2
related_notes:
  - "[[galaxy-collection-semantics]]"
  - "[[galaxy-collection-tools]]"
  - "[[nextflow-workflow-io-semantics]]"
  - "[[nextflow-params-to-galaxy-inputs]]"
  - "[[nextflow-path-glob-to-galaxy-datatype]]"
  - "[[nextflow-to-galaxy-channel-shape-mapping]]"
  - "[[nextflow-to-galaxy-reference-data-mapping]]"
related_molds:
  - "[[nextflow-summary-to-galaxy-interface]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
sources:
  - "Galaxy PR #19305 (Implement Sample Sheets), merged 2025-07-30"
  - "lib/galaxy/model/dataset_collections/types/sample_sheet.py"
  - "lib/galaxy/model/dataset_collections/types/sample_sheet_util.py"
  - "lib/galaxy/model/dataset_collections/type_description.py"
  - "lib/galaxy/schema/schema.py (SampleSheetColumnDefinition, SampleSheetRow)"
  - "lib/galaxy/tools/wrappers.py (DatasetCollectionWrapper.sample_sheet_row)"
  - "lib/galaxy/tools/sample_sheet_to_tabular.xml"
  - "lib/galaxy/webapps/galaxy/api/dataset_collections.py (sample_sheet_workbook endpoints)"
  - "lib/galaxy/model/migrations/alembic/versions_gxy/3af58c192752_implement_sample_sheets.py"
summary: "Galaxy's sample_sheet collection family: typed column metadata, four variants, mapping rules, validator allowlist."
---

# Galaxy sample_sheet collection types

Reference for the Galaxy backend shape that targets structured per-row metadata — the natural landing zone for Nextflow `samplesheetToList` parameters and for any source-side idiom that pairs typed metadata columns with dataset references.

## Shape

A `sample_sheet` is a list-shaped collection where each element carries a typed `columns` row, and the parent collectio
...

SKILL.md


# freeform-summary-to-galaxy-data-flow

Follow the procedure below and use the artifact/reference sections as the runtime contract.

## When To Use

- Translate a free-form source summary into a Galaxy data-flow design brief.

## Inputs

- Read artifact `freeform-summary`. Produced by `interview-to-freeform-summary`, `summarize-paper`. Free-form source summary emitted by summarize-paper or interview-to-freeform-summary; consumed alongside the Galaxy interface brief.
- Read artifact `freeform-galaxy-interface`. Produced by `freeform-summary-to-galaxy-interface`. Preceding Galaxy interface brief from freeform-summary-to-galaxy-interface that pins inputs, outputs, and labels.
- Read artifact `open-requirements-ledger`. Produced by `advance-galaxy-draft-step`, `apply-galaxy-workflow-changeset`, `compare-against-iwc-exemplar`, `cwl-summary-to-galaxy-data-flow`, `cwl-summary-to-galaxy-interface`, `cwl-summary-to-galaxy-template`, `freeform-summary-to-galaxy-data-flow`, `freeform-summary-to-galaxy-interface`, `freeform-summary-to-galaxy-template`, `implement-galaxy-tool-step`, `interview-to-galaxy-workflow-changeset`, `mature-galaxy-workflow-for-iwc`, `nextflow-summary-to-galaxy-data-flow`, `nextflow-summary-to-galaxy-interface`, `nextflow-summary-to-galaxy-reference-data`, `nextflow-summary-to-galaxy-template`, `repair-galaxy-draft-topology`. Carried obligations ledger open-requirements-ledger: the run's open, resolved, and surrendered entries with their provenance. Absent on the first Mold of a run; start an empty one.

## Outputs

- Write artifact `freeform-galaxy-data-flow` as `freeform-galaxy-data-flow.md`. Format: `markdown`. Reviewable Markdown brief: abstract operations, collection map/reduce choices, shape-changing placeholder steps, unresolved Galaxy tool needs, confidence, open questions.
- Write artifact `open-requirements-ledger` as `open-requirements.ledger.yml`. Format: `yaml`. Carried obligations ledger re-emitted by this step: entries it appended or closed updated, every other entry passed through with its provenance intact.

## Required Tools

- None declared. Procedure should not assume external CLIs are present.

## Load Upfront

- `references/notes/galaxy-data-flow-draft-contract.md`: Research note copied verbatim into the bundle. Keep the data-flow brief separate from gxformat2 templating and concrete step implementation.
- `references/notes/open-requirements-ledger.md`: Research note copied verbatim into the bundle. Inherit open entries rather than re-deriving them, close the ones this brief's wiring and collection decisions settle, and append data-flow obligations the narrative leaves open — a described transformation with no named tool, an implied intermediate the source never states, an ordering the prose doesn't fix.

## Load On Demand

- `references/patterns/galaxy-collection-patterns.md`: Pattern note copied verbatim into the bundle. Ground collection-shape choices in curated, corpus-observed operation and recipe patterns. Use when: selecting collection cleanup, reshape, identifier, or collection-tabular bridge patterns.
- `references/patterns/galaxy-conditionals-patterns.md`: Pattern note copied verbatim into the bundle. Ground conditional-branch and optional-step choices in curated, corpus-observed Galaxy when/pick_value patterns. Use when: data-flow translation needs optional steps, gating on non-empty results, routing between alternative outputs, or transform-or-pass-through branches.
- `references/patterns/galaxy-interval-patterns.md`: Pattern note copied verbatim into the bundle. Ground genomic-interval operation choices in curated, corpus-observed Galaxy interval recipes. Use when: the workflow operates on genomic intervals (BED/GFF/VCF coordinate features) and data-flow translation needs overlap, merge, coverage, windowing, masking, or set-algebra steps.
- `references/patterns/galaxy-tabular-patterns.md`: Pattern note copied verbatim into the bundle. Ground tabular bridge and table-operation choices in curated, corpus-observed operation patterns. Use when: data-flow translation needs filtering, joining, aggregation, pivoting, or tabular-collection bridges.
- `references/notes/galaxy-sample-sheet-collections.md`: Research note copied verbatim into the bundle. Preserve per-row metadata on the data-flow side: keep sample_sheet column_definitions wired through identifier-keyed steps instead of dropping into parallel parameter inputs, and re-attach metadata after map-over steps that lose it. Use when: the interface brief carries a sample_sheet[:paired|:paired_or_unpaired|:record] input, or the free-form summary describes per-sample/per-record metadata that must survive map-over steps.

## Validation

- None declared.

## Procedure

Read a free-form source summary plus the preceding Galaxy interface brief and emit a reviewable Markdown data-flow brief. Capture abstract operations, collection map/reduce choices, shape-changing placeholder transformations, unresolved Galaxy tool needs, confidence, and open questions.

Free-form sources rarely give enough to fix exact operations. Translate what the summary and interface brief support, classify the rest as unresolved tool needs or open questions, and do not present narrative intent as already-decided Galaxy wiring.

The output is not gxformat2 and should not resolve exact Tool Shed tools. freeform-summary-to-galaxy-template turns this handoff and the interface brief into a skeleton.

## Feedback Mode

- Feedback mode is off unless the caller explicitly enables `--feedback` or supplies a feedback-ledger path.
- When enabled, read `_feedback.md` before doing the work and use its registered `foundry-feedback.ledger.yml` protocol.
- Preserve harness-owned run and phase state. Append only concrete observations about a canonical Foundry source asset or a related project that this run showed to be at fault; do not put ordinary workflow requirements in this ledger.
- Before reporting completion, make one explicit pass over the work you just did. Do not ask yourself whether anything was unclear — recall what happened: where you guessed at something the instructions should have settled, needed information this bundle does not carry, hit an instruction that contradicted another or contradicted the artifacts in front of you, used a packaged reference that did not cover your case, or did something the procedure never describes.
- Append an entry for each such event that clears the protocol's bar. If none do, append nothing and report `no feedback` explicitly. Silence and a clean pass are not the same thing, and nothing downstream can tell them apart unless you say which one it was.
- Pass the same ledger path to any subagent used for this work, and merge updates serially so one writer cannot overwrite another.

## Runtime Notes

- Do not read Foundry source files at runtime; use only files packaged in this skill bundle and user-supplied artifacts.
- Preserve declared artifact filenames unless the user or harness supplies explicit paths.
- Carry unresolved assumptions into the output artifact instead of silently inventing missing source evidence.